Biochem Exam 461, Section I - Redox, Bioenergetics, Amino Acids, Acid-Base Chem - Prof. Ja, Exams of Biochemistry

Download Biochem Exam 461, Section I - Redox, Bioenergetics, Amino Acids, Acid-Base Chem - Prof. Ja and more Exams Biochemistry in PDF only on Docsity! 1 Biochemistry 461, Section I Your Printed Name:________________________________ February 27, 1997 Exam #1 Your SS#:________________________________ Prof. Jason D. Kahn Your Signature:________________________________ You have 80 minutes for this exam. Exams written in pencil or erasable ink will not be re-graded under any circumstances. Some information which may be useful is provided on the bottom half of the next page. Explanations should be concise, a couple of sentences. You will need a calculator for this exam, and no other study aids or materials are permitted. Useful Information: Ka = [H+][A-]/[HA] for the dissociation of HA, so pH = pKa + log ([A-]/[HA]) Kw = 10-14 = [HO-][H+] RT = 2476 J/mole today DG = DG°¢ + RTlnQ, where Q has the form of an equilibrium constant DG = -nFDE, where F = 96500 J/(V•mole), n = number of electrons transferred NA = 6.02 ¥ 1023 particles per mole 2 1. (18 pts) Redox reactions and the Nernst equation. The oxidation of NADH by sulfate can be used to create a proton gradient, which ATP synthase then taps to make ATP, as in the sketch to the right. The relevant standard reduction potentials at pH 7 are given below. NAD+ + H+ + 2 e- NADH E°¢ = –0.315 V SO42- + 2H+ + 2 e- SO32- + H2O E°¢ = 0.48 V (a; 8 pts) Write the balanced equation for this redox reaction, calculate DE°¢ and DG°¢, and calculate the equilibrium constant for the reaction. (b; 6 pts) If the pH is 5 on the inside of the compartment and 7 on the outside, what is DG for moving a proton into the compartment? (Ignore any membrane potentials.) How many protons can be pumped per NADH oxidized? 5 3. (20 points) Amino acids, peptides, and hydrogen bonding. (a; 10 pts) Draw the covalent structure of the tripeptide Tyr-Lys-Leu, with all functional groups in their predominant ionic forms at pH 7. Indicate which protons would be removed at pH 12, which is above the pKa of all ionizable side chains except Arg. Write the 1-letter code for each of the three amino acids below the structure. (b; 3 pts) Which amino acid provides biological buffering capacity? Why? Name the two sulfur- containing amino acids (full names for all three, please). (c; 7 pts) On the picture of adenosine at the right, circle the H’s which can be donated in hydrogen bonds. Draw in a plausible structure for the asparagine side chain making two hydrogen bonds to the adenine ring. O HO OH N N N N N HO H H H H Adenine Ring 6 4. (22 points) Secondary structure and the Ramachandran plot. (a; 4 pts) On the left extended polypeptide below, indicate which four atoms define the Y angle for amino acid i, which is bracketed by the dashed lines. On the right side indicate which four atoms define the F angle. On the left-hand diagram, draw two parallelograms indicating which sets of atoms are constrained to lie in a plane. N Cai N Cai+1 O H R OH H Cai-1 N Cai N Cai+1 O H R OH H Cai-1 Y F (b; 8 pts) Draw in three residues of the antiparallel b-sheet partner below the extended polypeptide chain drawn here. Include backbone hydrogen bonds and indicate where the next strand (i.e. if you were to draw a third one) would H-bond. Indicate side chains with R. Indicate the N terminus and the C terminus of the strand you draw. N N H R OH H N N O H R OH H R H O R H 7 (c; 8 pts) Discuss how a-helices and b-sheets can exhibit “sidedness”, i.e. asymmetric chemical properties, in different ways. Draw sketches to illustrate. (d; 2 pts) Name the 3-D molecule viewer program used in the in class computer demonstrations of secondary structure.